scholarly journals Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain

2003 ◽  
Vol 100 (12) ◽  
pp. 7158-7162 ◽  
Author(s):  
S. W. Roy ◽  
A. Fedorov ◽  
W. Gilbert
Keyword(s):  
Large Scale ◽  
Intron Loss ◽  
Mammalian Genes

scholarly journals Genetic and Molecular Analysis of Region 88E9;88F2 in Drosophila melanogaster, Including the ear Gene Related to Human Factors Involved in Lineage-Specific Leukemias

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1051-1065
Author(s):  
Claudia B Zraly ◽  
Yun Feng ◽  
Andrew K Dingwall
Keyword(s):  
Large Scale ◽  
Drosophila Genome ◽  
Embryonic Cells ◽  
Ems Mutagenesis ◽  
Recessive Lethal ◽  
Protein Levels ◽  
Late Embryogenesis ◽  
Complementation Groups ◽  
Mammalian Genes ◽  
Map Location

Abstract We identified and characterized the Drosophila gene ear (ENL/AF9-related), which is closely related to mammalian genes that have been implicated in the onset of acute lymphoblastic and myelogenous leukemias when their products are fused as chimeras with those of human HRX, a homolog of Drosophila trithorax. The ear gene product is present in all early embryonic cells, but becomes restricted to specific tissues in late embryogenesis. We mapped the ear gene to cytological region 88E11-13, near easter, and showed that it is deleted by Df(3R)ea5022rx1, a small, cytologically invisible deletion. Annotation of the completed Drosophila genome sequence suggests that this region might contain as many as 26 genes, most of which, including ear, are not represented by mutant alleles. We carried out a large-scale noncom-plementation screen using Df(3R)ea5022rx1 and chemical (EMS) mutagenesis from which we identified sevenc novel multi-allele recessive lethal complementation groups in this region. An overlapping deficiency, Df(3R)Po4, allowed us to map several of these groups to either the proximal or the distal regions of Df(3R)ea5022rx1. One of these complementation groups likely corresponds to the ear gene as judged by map location, terminal phenotype, and reduction of EAR protein levels.

scholarly journals The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xu Wang ◽  
Lihua Jia ◽  
Mingdao Wang ◽  
Hao Yang ◽  
Mingyue Chen ◽  
...  
Keyword(s):  
Large Scale ◽  
Core Protein ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Purifying Selection ◽  
Intron Loss ◽  
Gene Rearrangements ◽  
Total Size ◽  
Medicinal Fungus ◽  
Taiwanofungus Camphoratus

Abstract Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development

Development ◽  
2000 ◽  
Vol 127 (8) ◽  
pp. 1737-1749 ◽  
Author(s):  
M.S. Ko ◽  
J.R. Kitchen ◽  
X. Wang ◽  
T.A. Threat ◽  
X. Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Disorders ◽  
Large Scale ◽  
Expression Patterns ◽  
Mammalian Development ◽  
Mouse Development ◽  
New Genes ◽  
Entry Points ◽  
Preimplantation Mouse ◽  
Mammalian Genes

Little is known about gene action in the preimplantation events that initiate mammalian development. Based on cDNA collections made from each stage from egg to blastocyst, 25438 3′-ESTs were derived, and represent 9718 genes, half of them novel. Thus, a considerable fraction of mammalian genes is dedicated to embryonic expression. This study reveals profound changes in gene expression that include the transient induction of transcripts at each stage. These results raise the possibility that development is driven by the action of a series of stage-specific expressed genes. The new genes, 798 of them placed on the mouse genetic map, provide entry points for analyses of human and mouse developmental disorders.

Natural antisense transcripts: sound or silence?

2005 ◽  
Vol 23 (2) ◽  
pp. 125-131 ◽  
Author(s):  
Andreas Werner ◽  
Ariane Berdal
Keyword(s):  
Antisense Rna ◽  
Large Scale ◽  
Regulatory Mechanism ◽  
Antisense Transcription ◽  
Antisense Transcripts ◽  
Naturally Occurring ◽  
Mammalian Genes ◽  
Gene Regulatory ◽  
Regulatory Potential ◽  
To Come

Antisense RNA was a rather uncommon term in a physiology environment until short interfering RNAs emerged as the tool of choice to knock down the expression of specific genes. As a consequence, the concept of RNA having regulatory potential became widely accepted. Yet, there is more to come. Computational studies suggest that between 15 and 25% of mammalian genes overlap, giving rise to pairs of sense and antisense RNAs. The resulting transcripts potentially interfere with each other’s processing, thus representing examples of RNA-mediated gene regulation by endogenous, naturally occurring antisense transcripts. Concerns that the large-scale antisense transcription may represent transcriptional noise rather than a gene regulatory mechanism are strongly opposed by recent reports. A relatively small, well-defined group of antisense or noncoding transcripts is linked to monoallelic gene expression as observed in genomic imprinting, X chromosome inactivation, and clonal expression of B and T leukocytes. For the remaining, much larger group of bidirectionally transcribed genes, however, the physiological consequences of antisense transcription as well as the cellular mechanism(s) involved remain largely speculative.

scholarly journals The evolution of chloroplast genome structure in ferns

Genome ◽  
2010 ◽  
Vol 53 (9) ◽  
pp. 731-738 ◽  
Author(s):  
Paul G. Wolf ◽  
Jessie M. Roper ◽  
Aaron M. Duffy
Keyword(s):  
Large Scale ◽  
Common Ancestor ◽  
Genome Structure ◽  
Intron Loss ◽  
Seed Plants ◽  
Plant Structure ◽  
The Core ◽  
Plastome Evolution ◽  
The Common ◽  
First Time

The plastid genome (plastome) is a rich source of phylogenetic and other comparative data in plants. Most land plants possess a plastome of similar structure. However, in a major group of plants, the ferns, a unique plastome structure has evolved. The gene order in ferns has been explained by a series of genomic inversions relative to the plastome organization of seed plants. Here, we examine for the first time the structure of the plastome across fern phylogeny. We used a PCR-based strategy to map and partially sequence plastomes. We found that a pair of partially overlapping inversions in the region of the inverted repeat occurred in the common ancestor of most ferns. However, the ancestral (seed plant) structure is still found in early diverging branches leading to the osmundoid and filmy fern lineages. We found that a second pair of overlapping inversions occurred on a branch leading to the core leptosporangiates. We also found that the unique placement of the gene matK in ferns (lacking a flanking intron) is not a result of a large-scale inversion, as previously thought. This is because the intron loss maps to an earlier point on the phylogeny than the nearby inversion. We speculate on why inversions may occur in pairs and what this may mean for the dynamics of plastome evolution.

scholarly journals De novo assembly, delivery and expression of a 101 kb human gene in mouse cells

2018 ◽  
Author(s):  
Leslie A. Mitchell ◽  
Laura H. McCulloch ◽  
Sudarshan Pinglay ◽  
Henri Berger ◽  
Nazario Bosco ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
De Novo ◽  
Regulatory Elements ◽  
Functional Study ◽  
Regulatory Sequences ◽  
Dna Assembly ◽  
Functional Evaluation ◽  
Mammalian Genomes ◽  
Mammalian Genes

AbstractDesign and large-scale synthesis of DNA has been applied to the functional study of viral and microbial genomes. New and expanded technology development is required to unlock the transformative potential of such bottom-up approaches to the study of larger mammalian genomes. Two major challenges include assembling and delivering long DNA sequences. Here we describe a pipeline for de novo DNA assembly and delivery that enables functional evaluation of mammalian genes on the length scale of 100 kb. The DNA assembly step is supported by an integrated robotic workcell. We assembled the 101 kb human HPRT1 gene in yeast, delivered it to mouse embryonic stem cells, and showed expression of the human protein from its full-length gene. This pipeline provides a framework for producing systematic, designer variants of any mammalian gene locus for functional evaluation in cells.Significance StatementMammalian genomes consist of a tiny proportion of relatively well-characterized coding regions and vast swaths of poorly characterized “dark matter” containing critical but much less well-defined regulatory sequences. Given the dominant role of noncoding DNA in common human diseases and traits, the interconnectivity of regulatory elements, and the importance of genomic context, de novo design, assembly, and delivery can enable large-scale manipulation of these elements on a locus scale. Here we outline a pipeline for de novo assembly, delivery and expression of mammalian genes replete with native regulatory sequences. We expect this pipeline will be useful for dissecting the function of non-coding sequence variation in mammalian genomes.

Some comments about observations and image processing of comet 29P/Schwassmann-Wachmann 1

1999 ◽  
Vol 173 ◽  
pp. 243-248
Author(s):  
D. Kubáček ◽  
A. Galád ◽  
A. Pravda
Keyword(s):  
Image Processing ◽  
Large Scale ◽  
Harvard College ◽  
Oak Ridge ◽  
Large Scale Structures ◽  
Short Period Comet ◽  
Short Period ◽  
Scale Structures ◽  
Harvard College Observatory ◽  
Period Comet

AbstractUnusual short-period comet 29P/Schwassmann-Wachmann 1 inspired many observers to explain its unpredictable outbursts. In this paper large scale structures and features from the inner part of the coma in time periods around outbursts are studied. CCD images were taken at Whipple Observatory, Mt. Hopkins, in 1989 and at Astronomical Observatory, Modra, from 1995 to 1998. Photographic plates of the comet were taken at Harvard College Observatory, Oak Ridge, from 1974 to 1982. The latter were digitized at first to apply the same techniques of image processing for optimizing the visibility of features in the coma during outbursts. Outbursts and coma structures show various shapes.

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